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ChangeLog
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23/09/14 -*- Version 2.2.0 -*-
23/09/14 Julien Dutheil
* Fixed bug #73
16/09/14 Julien Dutheil
* Fixed bug #79
24/07/14 Julien Dutheil
* Alphabet code gets a refreshment!
05/03/13 -*- Version 2.1.0 -*-
07/02/13 Julien Dutheil
* StateProperties => Alphabet index (dir renamed).
* New BppO classes forAlphabet Index 1 and 2, and corresponding methods in SequenceApplicationTools.
19/01/13 Julien Dutheil
* Compiles with -Wconversion.
09/01/13 Julien Dutheil
* Use size_t instead of unsigned int for indexes in containers.
17/09/12 Julien Dutheil
* Reorganized IO classes.
11/09/12 Julien Dutheil
* Added generic container converter function.
30/07/12 Julien Dutheil
* Moved features, fastq and maf to new bpp-seq-omics library.
18/07/12 Julien Dutheil
* Bug fixed in merge maf iterator, in case a sequence is missing in one of the two blocks.
25/06/12 Julien Dutheil
* Extended maf tools and reorganization of the code.
* Extended GFF output.
* New [] operator in SequenceFeatureSet.
18/06/12 Julien Dutheil
* Fixed bug in Maf parser: scores are now parsed correctly.
08/03/12 Julien Dutheil
* Added support for '*' character in proteins (stop codon)
09/02/12 -*- Version 2.0.3 -*-
16/01/12 Julien Dutheil
* Bug #42 solved, new support for extended fasta parser in application tools.
* Added contribution from Benoit Nabholz and Annabelle Haudry on 4-fold degenerated sites.
06/01/12 Julien Dutheil
* Added support for "!" state in nucleic alphabet, which can be either a gap or an unknown character.
24/11/11 Julien Dutheil
* Added SequenceWalker class and test.
22/11/11 Sylvain Gaillard
* Added support for FastQ
21/11/11 Julien Dutheil
* Added support for GFF3.
21/11/11 Sylvain Gaillard
* Bug #35 solved.
18/11/11 Julien Dutheil
* New MafIterators: SequenceStatistics and PairwiseSequenceStatistics.
* Function SequenceTools::getPercentIdentity now allows to exclude gaps.
15/09/11 Julien Dutheil
* Merge function of SequenceWithAnnotation now also merges annotations properly.
17/06/11 Julien Dutheil
* Bug #39 solved.
09/06/11 -*- Version 2.0.2 -*-
08/06/11 Julien Dutheil
* Fixed several Maf iterators.
28/02/11 -*- Version 2.0.1 -*-
* Fixed debian packaging.
07/02/11 -*- Version 2.0.0 -*-
19/11/10 Julien Dutheil
* Solved bug 0000016 (General comments not copied in containers).
* A few more code cleaning.
01/11/10 Julien Dutheil
* Solved bug 0000005 (Clustal parser).
* Added unit testing for sequence input format.
* Solved bug 0000004 (Remove gap sites in SiteContainer).
12/10/10 Benoît Nabholz
* Added yeast mitochondrial codon alphabet and genetic code.
20/09/10 Julien Dutheil
* Reorganization of the code for version 2.0.
06/09/10 Julien Dutheil
* Added support for masked sequences in SequenceWithAnnotationTools and MafParser.
05/09/10 Julien Dutheil
* First draft of CaseMaskedAlphabet, for dealing with repeat-masked sequences for instance.
21/07/10 Julien Dutheil
* Added method hasSequence(name) in SequenceContainer interface.
20/07/10 Julien Dutheil
* New Sequence interface design.
* Maf parser now reads quality scores if there are some.
19/07/10 Julien Dutheil
* New method isInit in CodonAlphabet.
* New method getCDS in SequenceTools.
28/04/10 Julien Dutheil
* New MAF genome alignment parser.
22/04/10 Sylvain Gaillard
* Break SequenceTools interface:
- renamed invert -> getInvert
- renamed complement -> getComplement
now invert and complement methods deals with sequence ref
- New method invertComplement
16/04/10 Julien Dutheil
* New Stockholm sequence format (output only).
* Refactoring of class ISequence2 => IAlignment + new interface OAlignment.
24/03/10 -*- Version 1.7.0 -*-
11/03/10 Julien Dutheil
* Nexus format now deals with lower case keywords.
17/12/09 Julien Dutheil
* Code cleaning for VectorSiteContainer
* New class CompressedVectorSiteContainer using less memory than
VectorSiteContainer, but more restricted.
16/11/09 Sylvain Gaillard
* No more "using namespace" in header files.
04/11/09 Julien Dutheil
* Remove SymbolListTools::randomizeContent to a more efficient SymbolList::shuffle
method.
12/10/09 Julien Dutheil
* Now SeqLib compiles with -Weffc++ and -Wshadow without any warning :)
22/09/09 Julien Dutheil
* Finally added 'addSequence' method in SequenceContainer.
* MapSequenceContainer now has a addSequence method that uses the name of the
sequence as a key by default.
* Several methods in Sequence/SiteContainerTools are not templated anymore and
have been improved.
09/09/09 Sylvain Gaillard
* Fixed white space skip in Fasta sequence
20/08/09 Julien Dutheil
* Added config files for CMake.
19/08/09 Sylvain Gaillard
* Introduced 3 new interfaces IOSequenceStream, ISequenceStream and
OSequenceStream. These interfaces are intended to be used by IOFormat
dealing with Sequence and not SequenceContainers. They are actually
implemented by the Fasta class.
17/08/09 Adam Smith
* Bug fixed in DefaultAlphabet: unknow state is 37 not 38.
04/08/09 Sylvain Gaillard
* Introduced new classes for Alphabet States
23/07/09 Sylvain Gaillard
* Added SequenceTools::getPutativeHaplotypes
22/07/09 Sylvain Gaillard
* Added SequenceTools::getNumberOfUnresolvedSites
* Updated SequenceTools::getNumberOfSites,
SequenceTools::getNumberOfCompleteSites and SequenceTools::removeGaps to be
Alphabet implementation independant.
07/07/07 Julien Dutheil
* Updated GranthamAAChemicalDistance, with a new signed, non-symmetric,
option.
26/06/09 Sylvain Gaillard
* Added new SequencePositionIterators classes.
23/06/09 Julien Dutheil
* Actualization of the Container classes: now returns references and not
pointer. Several code updates, including copy contructors.
17/06/09 Sylvain Gaillard (Glasgow Workshop)
* Fix DNA/RNA/ProteicAlphabet::getAlias: works now with lower case states.
* Fix SiteTools::isConstant test gap or unknown
* Turning SequenceContainerTools::getFrequencies into void function.
21/07/08 -*- Version 1.6.0 -*-
28/05/09 Julien Dutheil
* Added basic support for the Nexus format.
22/05/09 Julien Dutheil
* Improved Clustal format (solves bug found by Emmanuel M.)
* SequenceApplicationTools uses the keyval syntax for format description.
27/04/09 Julien Dutheil
* Added site randomization method.
28/02/09 Julien Dutheil
* Added mutual information calculation.
* Added pairwise counting methods.
* Frequencies counting methods have been improved (avoid useless copy of maps).
16/01/09 Julien Dutheil
* max_gap_allowed option in SequenceApplicationTools is now a included bound:
0 or 0% will keep all complete sites, and 'n=number of sequences' or 100%
will keep all sites.
13/01/09 Sylvain Gaillard
* Little optimization in Fasta::write() method.
12/01/09 Sylvain Gaillard
* Added support for comments (HUPO-PSI like) in Fasta.
08/01/09 Julien Dutheil
* SequenceTools::reverse method has been deprecated in favor of the
SequenceTools::inverse method, of witch it is now an alias.
07/01/09 Julien Dutheil
* Code improvement in Vector containers.
21/12/08 Julien Dutheil
* Return type for clone() methods corrected (Sequence, Site, SiteContainer and derivated classes).
* Bug fixed in SequenceApplicationTools::get[Sequence/Site]Container, phylip format.
21/07/08 -*- Version 1.5.0 -*-
05/12/08 Julien Dutheil
* VectorSiteContainer::getSite() faster (more than 10 times faster on a ~500
sequences data set!)
04/12/08 Julien Dutheil
* Fixed missing redefinition of translate and reverse methods in class DNAToRNA.
* Made inheritance virtual.
01/12/08 Julien Dutheil
* New methods getSupportedInts and getSupportedChars in Alphabet classes.
18/11/08 Julien Dutheil
* biopp-help-forum 91 (by Stephen Smith): Fasta, Mase, Clustal and Phylip now
have an option to turn off the name checking and decrease loading time.
* biopp-help-forum 93 (by Stephen Smith): Phylip format now supports any
delimiter when reading/writing files in extended format.
14/11/08 Sylvain Gaillard
* New method SequenceTools::subtractHaplotype(Sequence, Sequence, string,
unsigned int).
07/11/08 Julien Dutheil
* New contructor in VectorSiteContainer now as a tag to disable position
checking, which can turn to be quite slow.
06/11/08 Sylvain Gaillard
* New class PhredPhd to read sequence from phd files produced by the phred
program
* Removed an unused method in PhredPoly
05/11/08 Sylvain Gaillard
* New methods Alphabet::getGeneric(states) implemented in AbstractAlphabet,
DefaultAlphabet, DNA, RNA and ProteicAlphabet.
* New alphabet exception CharStateNotSupportedException.
* New class PhredPoly to read sequence from poly files produced by the phred
program.
* Fixed heterozygous site read in PhredPoly.
09/10/08 Julien Dutheil
* New method SequenceTools::invert(Sequence).
24/09/08 Bastien Boussau & Julien Dutheil
* Memory leak fixed in Fasta and Mase readers.
21/07/08 -*- Version 1.4.1 -*-
26/06/08 Julien Dutheil
* Bug fixed in Clustal format.
20/04/08 Julien Dutheil
* New interface ISequence2 for reading alignments.
18/03/08 Julien Dutheil and Bastien Boussau
* Bowker's test for homogeneity implemented in SequenceTools.
08/02/08 Julien Dutheil
* Bug fixed in VectorSequenceContainer: method addSequence is now virtual!
(thanks to Laurent Gueguen for pointing out this bug)!.
07/02/08 Julien Dutheil
* Added function isDNAAlphabet and isRNAAlphabet in AlphabetTools.
* Bug fixed in getAlphabetFromSequence method.
* Method getContent in Sequence and Site now outputs a reference.
18/01/08 -*- Version 1.4.0 -*-
09/01/08 Julien Dutheil
* All classes included in the new 'bpp' namespace.
06/11/07 Julien Dutheil
* New function SequenceContainerTools::merge.
02/10/07 Julien Dutheil
* New class GenBank, enabling GenBank sequence format support for input.
* Added new copy constructors from SequenceContainer in
Vector[Site/Sequence]Container.
* New methods changeUnresolvedCharacterToGaps and changeGapsToUnknownCharacters in SymbolListTools.
* Bug fixed in changeUnresolvedCharacterToGaps in SiteContainerTools.
06/07/07 -*- Version 1.3.0 -*-
12/06/07 Julien Dutheil
* More tools in class alphabet (isGap, isUnresolved, etc.)
* New class DistanceMatrix, previously in phyllib.
* New similarity measures in SiteContainerTools.
04/06/07 Julien Dutheil
* New constructor from sequence names in VectorSiteContainer.
01/06/07 Julien Dutheil
* New method SiteContainerTools::boostrapSites to bootstrap an alignment.
21/05/07 Julien Dutheil
* New method SequenceContainerTools::getSequenceContainer to read non-aligned
sequences.
04/05/07 Julien Dutheil
* Bug fixed in global alignment with gap opening and extending penalties.
* New generic score scheme.
* Compatibility update (NumCalc)
24/04/07 Benoît Nabholz & Julien Dutheil
* GeneticCode classes can now translate unknow codons to unknown amino acids.
02/04/07 Julien Dutheil
* VIRTUAL_COV variable changed to NO_VIRTUAL_COV. configure.ac file updated.
=> Default behaviour is now /really/ to use covariant return type with
virtual inheritence, even when importing the files in an IDE. To use the old
compilers behaviour, one must set the NO_VIRTUAL_COV preproc variable.
* this modification also solves a problem with the old configure.ac which
was not correctly updated in version 1.2.0 :(
* Bug fixed in SymbolListTools::getCounts.
02/04/07 Julien Dutheil
* New method getAlphabetIndex1() in class SimpleIndexDistance.
24/02/07 Julien Dutheil
* New pairwise alignment algorithm: gap opening and extending penalties.
22/02/07 Julien Dutheil
* GeneticCode derivated classes now properly redefine the translate(Sequence&)
method.
19/01/07 -*- Version 1.2.0 -*-
19/01/07 Julien Dutheil
* Functions AlphabetTools::getType() and StringSequenceTools::getAlphabetFromSequence() rewritten.
* New DefaultNucleotideScore matrix.
* New AAIndex1Entry and AAIndex2Entry classes which create AlphabetIndex1 and
AlphabetIndex2 objects from AAIndex1 and AAIndex2 entries, respectively.
18/12/06 Julien Dutheil
* New alignment tools in SiteContainerTools, including the Needleman and
Wunsch alogrithm.
* BLOSUM50 matrix available.
* Bug fixed in Sequence.h: method setContent is now properly redefined.
* Bug fixed in ProteicAlphabet->getAbbr(int). The returned result is now
correct!!!
06/12/06 Julien Dutheil
* DefaultAlphabet now accepts "." characters.
* New AlphabetTools::isDefaultAlphabet(const Alphabet *) method.
* New SiteContainerTools::resolveDottedAlignment(const Sitecontainer &, const Alphabet *) method.
30/08/06 Julien Dutheil
* Bug fixed in phylip sequential reader, + duplicated sequence in container
now throws sequence name. (included in 1.1.1 release).
28/08/06 -*- Version 1.1.1 -*-
08/08/06 Julien Dutheil
* Bug fixed in Phylip sequential read method.
15/06/06 Julien Dutheil
* Method changeGapsToUnknownCharacters() moved from SequenceContainerTools to
SiteContainerTools, and is really faster!
* New removeGapOnlySites() method in SiteContainerTools.
* New method SiteTools::isGapOnly().
* new 'sequence.max_gap_allowed' option in SequenceApplicationTools::getSitesToAnalyse().
13/06/06 Julien Dutheil
* Phylip sequential format improved, no more empty line between sequences
needed.
12/06/06 Julien Dutheil
* SiteTools::isConstant() method now has a 'ignoreUnknown' option.
01/01/06 Julien Dutheil
* VectorSiteContainer and AlignedSequenceContainer now number sites from 1 (and not 0).
17/05/06 Benoît Nabholz, Sylvain Glémin & Julien Dutheil
* Bug fixed in SiteContainerTools::getConsensus(), + SymbolListTools::getFrequencies() and getCounts() improved.
15/05/06 Julien Dutheil
* Bug fixed: Added getUnknownCharacterCode() method in DefaultAlphabet.
09/05/06 Julien Dutheil
* New AAChargeIndex class.
* Bug fixed in SiteTools::hasUnknown(Site).
18/04/06 -*- Version 1.1.0 -*-
18/04/06 Julien Dutheil
* New IOSequenceFactory class.
06/04/06 Julien Dutheil
* New () function operators defined on SequenceContainers.